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1. High-throughput plant phenotyping: a role for metabolomics?

Author:
Robert D. Hall; John C. D’Auria; Antonio C. Silva Ferreira; Yves Gibon; Dariusz Kruszka; Puneet Mishra; Rick van de Zedde
Source:
Trends in plant science 2022 v.27 no.6 pp. 549-563
ISSN:
1360-1385
Subject:
genotype-phenotype correlation,   etc   ; metabolites; metabolomics; phenotype;     Show all 4 Subjects
Abstract:
... High-throughput (HTP) plant phenotyping approaches are developing rapidly and are already helping to bridge the genotype–phenotype gap. However, technologies should be developed beyond current physico-spectral evaluations to extend our analytical capacities to the subcellular level. Metabolites define and determine many key physiological and agronomic features in plants and an ability to integrate ...
DOI:
10.1016/j.tplants.2022.02.001

2. MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect

Author:
Ammar Tareen; Mahdi Kooshkbaghi; Anna Posfai; William T. Ireland; David M. McCandlish; Justin B. Kinney
Source:
Genome biology 2022 v.23 no.1 pp. 98
ISSN:
1474-760X
Subject:
genotype-phenotype correlation,   etc   ; computer software; data collection; genes;     Show all 4 Subjects
Abstract:
... Multiplex assays of variant effect (MAVEs) are a family of methods that includes deep mutational scanning experiments on proteins and massively parallel reporter assays on gene regulatory sequences. Despite their increasing popularity, a general strategy for inferring quantitative models of genotype-phenotype maps from MAVE data is lacking. Here we introduce MAVE-NN, a neural-network-based Python ...
DOI:
10.1186/s13059-022-02661-7

3. Multi-donor × elite-based populations reveal QTL for low-lodging wheat

Author:
M. Fernanda Dreccer; Bethany Macdonald; Claire A. Farnsworth; M. Valeria Paccapelo; Mary Anne Awasi; Anthony G. Condon; Kerrie Forrest; Ian Lee Long; C. Lynne McIntyre
Source:
Theoretical and applied genetics 2022 v.135 no.5 pp. 1685-1703
ISSN:
0040-5752
Subject:
genetic correlation,   etc   ; cultivars; genotyping; germplasm; heritability; phenotype; wheat;     Show all 7 Subjects
Abstract:
... KEY MESSAGE: Low-lodging high-yielding wheat germplasm and SNP-tagged novel alleles for lodging were identified in a process that involved selecting donors through functional phenotyping for underlying traits with a designed phenotypic screen, and a crossing strategy involving multiple-donor × elite populations. Lodging is a barrier to achieving high yield in wheat. As part of a study investigatin ...
DOI:
10.1007/s00122-022-04063-6

4. Genetic Correlation, Pleiotropy, and Molar Morphology in a Longitudinal Sample of Australian Twins and Families

Author:
Kathleen S. Paul; Christopher M. Stojanowski; Toby Hughes; Alan H. Brook; Grant C. Townsend
Source:
Genes 2022 v.13 no.6 pp. -
ISSN:
2073-4425
Subject:
genetic correlation,   etc   ; anthropology; data collection; humans; pleiotropy; statistical analysis; teeth; variance; Arizona;     Show all 9 Subjects
Abstract:
... This study aims to expand our understanding of the genetic architecture of crown morphology in the human diphyodont dentition. Here, we present bivariate genetic correlation estimates for deciduous and permanent molar traits and evaluate the patterns of pleiotropy within (e.g., m1–m2) and between (e.g., m2–M1) dentitions. Morphology was observed and scored from dental models representing participa ...
DOI:
10.3390/genes13060996

5. Probing the glycans accessibility in the nanoparticle biomolecular corona

Author:
Eva Clemente; Marta Martinez-Moro; Duong N Trinh; Mahmoud G. Soliman; Daniel I R Spencer; Richard A Gardner; Maximilianos Kotsias; Ana Sánchez Iglesias; Sergio Moya; Marco P Monopoli
Source:
Journal of colloid and interface science 2022 v.613 pp. 563-574
ISSN:
0021-9797
Subject:
fluorescence correlation spectroscopy,   etc   ; blood plasma; citrates; lectins; macrophages; nanogold; polysaccharides; protein corona; proteomics;     Show all 9 Subjects
Abstract:
... Following blood administration, the pristine surface of nanoparticles (NPs) associates with biomolecules from the surrounding environment forming the so-called “biomolecular corona”. It is well accepted that the biomolecular corona dramatically affects the NP fate in the biological medium while the pristine surface is no longer available for binding. Recent studies have shown that the glycans asso ...
DOI:
10.1016/j.jcis.2021.11.140

6. First genetic evaluation of growth traits in Larimichthys polyactis to guide the formulation of selective breeding programs

Author:
Feng Liu; Wei Zhan; Qingping Xie; Bao Lou; Mingming Han; Wantu Xu; Shunshun Tao
Source:
Aquaculture 2022 v.554 pp. 738141
ISSN:
0044-8486
Subject:
genetic correlation,   etc   ; Larimichthys polyactis; aquaculture; body length; body weight; genetic improvement; genetic variation; heritability; phenotype;     Show all 9 Subjects
Abstract:
... Growth is an economically important trait in aquaculture. For the genetic improvement of growth traits in Larimichthys polyactis, a relatively new aquaculture species with great potential in large-scale farming, a genetic evaluation of these traits is necessary. In the present study, 34 families of L. polyactis were used to estimate genetic parameters for body weight, total length, and body length ...
DOI:
10.1016/j.aquaculture.2022.738141

7. Genotype affects free amino acids of egg yolk and albumen in Japanese indigenous breeds and commercial Brown layer chickens

Author:
Tatsuhiko Goto; Kosei Ohya; Masahiro Takaya
Source:
Poultry science 2022 v.101 no.2 pp. 101582
ISSN:
0032-5791
Subject:
phenotypic correlation,   etc   ; egg quality; egg shell; egg yolk; eggs; free amino acids; genetic background; phenotype;     Show all 8 Subjects
Abstract:
... Using a variety of genetic resources, the aim of this study is to see how genetic background affects egg traits in chickens. Three different chicken genotypes (a commercial Brown layer, BOR; 2 Japanese indigenous breeds, NGY and YKD) were investigated effects on genotype in 10 external and internal egg quality traits along with 20 yolk and albumen free amino acid traits. Significant effects on gen ...
DOI:
10.1016/j.psj.2021.101582

8. H1299R Variant in Factor V and Recurrent Pregnancy Loss: A Systematic Review and Meta-Analysis Protocol

Author:
Alessio Ardizzone; Anna Paola Capra; Stefania Mondello; Silvana Briuglia; Maria Angela La Rosa; Michela Campolo; Emanuela Esposito
Source:
Genes 2022 v.13 no.6 pp. -
ISSN:
2073-4425
Subject:
genotype-phenotype correlation,   etc   ; females; genes; genotyping; heterozygosity; homozygosity; meta-analysis; pregnancy; protocols; risk; systematic review;     Show all 11 Subjects
Abstract:
... Recurrent pregnancy loss (RPL) is defined as the loss of two or more pregnancies, affecting approximately 1 to 3% of women worldwide. Scientific data highlight a possible correlation between thrombophilic genetic variants and RPL. H1299R variant in the factor V gene would lead to an increased thrombotic risk associated with frequent miscarriages. However, the data are often conflicting, making thi ...
DOI:
10.3390/genes13061019

9. Heritability of perching behavior and its genetic relationship with incidence of floor eggs in Rhode Island Red chickens

Author:
Anna Wolc; Petek Settar; Janet E. Fulton; Jesus Arango; Kaylee Rowland; Danny Lubritz; Jack C. M. Dekkers
Source:
Genetics, selection, evolution 2021 v.53 no.1 pp. 38
ISSN:
1297-9686
Subject:
genetic correlation; phenotypic correlation,   etc   ; Rhode Island Red; genetic relationships; genetic selection; heritability; models; temperament;     Show all 8 Subjects
Abstract:
... BACKGROUND: As cage-free production systems become increasingly popular, behavioral traits such as nesting behavior and temperament have become more important. The objective of this study was to estimate heritabilities for frequency of perching and proportion of floor eggs and their genetic correlation in two Rhode Island Red lines. RESULTS: The percent of hens observed perching tended to increase ...
DOI:
10.1186/s12711-021-00630-5

10. Expanding Phenotype of Poirier–Bienvenu Syndrome: New Evidence from an Italian Multicentrical Cohort of Patients

Author:
Alessandro Orsini; Andrea Santangelo; Francesca Bravin; Alice Bonuccelli; Diego Peroni; Roberta Battini; Thomas Foiadelli; Veronica Bertini; Angelo Valetto; Michele Iacomino; Vincenzo Nigro; Anna Laura Torella; Marcello Scala; Valeria Capra; Maria Stella Vari; Anna Fetta; Veronica Di Pisa; Francesca Montanari; Roberta Epifanio; Paolo Bonanni; Roberto Giorda; Francesca Operto; Grazia Pastorino; Esra Sarigecili; Esra Sardaroglu; Cetin Okuyaz; Sevgan Bozdogan; Luciana Musante; Flavio Faletra; Caterina Zanus; Alessandro Ferretti; Federico Vigevano; Pasquale Striano; Duccio Maria Cordelli
Source:
Genes 2022 v.13 no.2 pp. -
ISSN:
2073-4425
Subject:
genotype-phenotype correlation,   etc   ; epilepsy; genes; genetic analysis; heterozygosity; mutation; neurons; patients; phenotype; retrospective studies; synaptic transmission;     Show all 11 Subjects
Abstract:
... Background: Poirier–Bienvenu Neurodevelopmental Syndrome (POBINDS) is a rare disease linked to mutations of the CSNK2B gene, which encodes for a subunit of caseinkinase CK2 involved in neuronal growth and synaptic transmission. Its main features include early-onset epilepsy and intellectual disability. Despite the lack of cases described, it appears that POBINDS could manifest with a wide range of ...
DOI:
10.3390/genes13020276

11. Genetic correlation between biopsied and post-mortem muscle fibre characteristics and meat quality traits in swine

Author:
Seung-Hoon Lee; Sangwook Kim; Jun-Mo Kim
Source:
Meat science 2022 v.186 pp. 108735
ISSN:
0309-1740
Subject:
genetic correlation,   etc   ; biopsy; color; drip loss; heritability; lean meat; marbling; meat; meat production; muscle fibers; swine;     Show all 11 Subjects
Abstract:
... Muscle fibre characteristics (MFCs) are related to lean meat production and meat quality. We newly estimated the heritability and genetic correlation of MFCs and meat quality in biopsied and post-mortem meat samples of 595 Jeju black pigs (JBPs). The cross-sectional area (CSA) (Type I: 0.76 and Type IIA: 0.89), % MF area (MFA) (Type I: 0.82), and % MF number (MFN) between the biopsied and post-mor ...
DOI:
10.1016/j.meatsci.2022.108735

12. Genetic Parameters of Workability Traits in the Population of Polish Holstein-Friesian Cows Based on Conventional and Genomic Data

Author:
Bartosz Szymik; Piotr Topolski; Wojciech Jagusiak
Source:
Animals 2021 v.11 no.8 pp. -
ISSN:
2076-2615
Subject:
genetic correlation; phenotypic correlation,   etc   ; Holstein; cows; data collection; genomics; genotype; lactation; models; pedigree; phenotype; sires; temperament;     Show all 13 Subjects
Abstract:
... Heritabilities of workability (WT) traits—milking speed (MS) and temperament (MT)—as well as genetic and phenotypic correlations between these traits in the population of Polish Holstein-Friesian (PHF) cows were estimated. The estimation of genetic parameters was performed twice: first with the use of pedigree data; and second with the use of pedigree and genomic data. Phenotypic data from routine ...
DOI:
10.3390/ani11082443

13. A note on stochastic complementarity for the applied researcher

Author:
Alessandro Iaria; Ao Wang
Source:
Economics letters 2021 v.199 pp. 109731
ISSN:
0165-1765
Subject:
correlation,   etc   ; economics; logit analysis; researchers;     Show all 4 Subjects
Abstract:
... In their discussion of stochastic complementarity, Manzini et al. (2018) show that the intuitively appealing correlation criterion does not—in general—satisfy the axiom of monotonicity: products classified as complements can turn into substitutes following an increase in their joint purchases. In this note, we show that, however, by restricting attention to mixed logit models along the lines of Ge ...
DOI:
10.1016/j.econlet.2021.109731

14. GWAS and genomic prediction of milk urea nitrogen in Australian and New Zealand dairy cattle

Author:
Irene van den Berg; Phuong N. Ho; Tuan V. Nguyen; Mekonnen Haile-Mariam; Iona M. MacLeod; Phil R. Beatson; Erin O’Connor; Jennie E. Pryce
Source:
Genetics, selection, evolution 2022 v.54 no.1 pp. 15
ISSN:
1297-9686
Subject:
genetic correlation,   etc   ; casein; evolution; genomics; meta-analysis; milk; nitrogen; prediction; quantitative traits; urea nitrogen; Australia; New Zealand;     Show all 12 Subjects
Abstract:
... BACKGROUND: Urinary nitrogen leakage is an environmental concern in dairy cattle. Selection for reduced urinary nitrogen leakage may be done using indicator traits such as milk urea nitrogen (MUN). The result of a previous study indicated that the genetic correlation between MUN in Australia (AUS) and MUN in New Zealand (NZL) was only low to moderate (between 0.14 and 0.58). In this context, an al ...
DOI:
10.1186/s12711-022-00707-9

15. Impact of a divergent selective breeding programme on individual feed conversion ratio in Nile tilapia Oreochromis niloticus measured in groups by video-recording

Author:
Hugues de Verdal; Pierrick Haffray; Vincent Douchet; Marc Vandeputte
Source:
Aquaculture 2022 v.548 pp. 737572
ISSN:
0044-8486
Subject:
genetic correlation,   etc   ; Oreochromis niloticus; feed conversion; feed intake; fish; fish consumption; heritability; juveniles; video recording; weight gain;     Show all 10 Subjects
Abstract:
... Feed conversion ratio (FCR) is an important trait to target in breeding programs in order to improve fish farming sustainability and increase environmental efficiency. Due to the complexity of accurately measuring the individual feed consumption of fish, developing a selective breeding programme to improve FCR is a challenge. Using video-recordings of several consecutive meals in tilapia groups, w ...
DOI:
10.1016/j.aquaculture.2021.737572

16. MEFV gene allele frequency and genotype distribution in 3230 patients’ analyses by next generation sequencing methods

Author:
Berkay Kırnaz; Yüksel Gezgin; Afig Berdeli
Source:
Gene 2022 v.827 pp. 146447
ISSN:
0378-1119
Subject:
genotype-phenotype correlation,   etc   ; DNA; Jews; familial Mediterranean fever; gene frequency; genes; heterozygosity; homozygosity; hospitals; medicine; mutation; patients;     Show all 12 Subjects
Abstract:
... Familial Mediterranean Fever (FMF, OMIM ID: 249100) is the most common autoinflammatory, autosomal recessive disease caused by mutations in the MEFV gene. It is widespread in the Mediterranean, primarily among Turkish, Armenian, Arab and Jewish. This study aims to examine genotype distributions of common MEFV variants in the Turkish population using targeted NGS and to evaluate all rare mutations. ...
DOI:
10.1016/j.gene.2022.146447

17. Genetics and breeding of a black-bone and blue eggshell chicken line. 2. Laying patterns and egg production in two consecutive generations

Author:
Huanhuan Wang; Avigdor Cahaner; Lifeng Lou; Lei Zhang; Ying Ge; Qinghai Li; Xuedong Zhang
Source:
Poultry science 2022 v.101 no.5 pp. 101679
ISSN:
0032-5791
Subject:
genetic correlation,   etc   ; animal models; cold stress; egg production; egg shell; egg weight; eggs; hens; heritability; phenotype; selection index;     Show all 11 Subjects
Abstract:
... The BG line was originated from the cross between 2 Chinese indigenous breeds, Dongxiang blue eggshell, and Jiangshan black-bone, and has been bred to combine dark heavy black-bone body and high production of blue-shell eggs, into single dual-purpose line. Full-pedigree hens from 2 generations, G4 (n = 441) and G5 (n = 464), were reared in the same single-cage laying facility in 2019–2020 and 2020 ...
DOI:
10.1016/j.psj.2021.101679

18. Addressing uncertainty in genome-scale metabolic model reconstruction and analysis

Author:
David B. Bernstein; Snorre Sulheim; Eivind Almaas; Daniel Segrè
Source:
Genome biology 2021 v.22 no.1 pp. 64
ISSN:
1474-760X
Subject:
genotype-phenotype correlation,   etc   ; genome; surveys; uncertainty;     Show all 4 Subjects
Abstract:
... The reconstruction and analysis of genome-scale metabolic models constitutes a powerful systems biology approach, with applications ranging from basic understanding of genotype-phenotype mapping to solving biomedical and environmental problems. However, the biological insight obtained from these models is limited by multiple heterogeneous sources of uncertainty, which are often difficult to quanti ...
DOI:
10.1186/s13059-021-02289-z

19. Impact of environmental disturbances on estimated genetic parameters and breeding values for growth traits in pigs

Author:
Vincent Le; Tom Rohmer; Ingrid David
Source:
Animal 2022 v.16 no.4 pp. 100496
ISSN:
1751-7311
Subject:
genetic correlation,   etc   ; animal models; average daily gain; body weight; climate change; farms; feed intake; heat stress; heritability; phenotype; piglets;     Show all 11 Subjects
Abstract:
... Due to the diversification of farming systems and climate change, farm animals are exposed to environmental disturbances to which they respond differently depending on their robustness. Disturbances such as heat stress or sanitary challenges (not always recorded, especially when they are of short duration and low intensity) have a transitory impact on animals, resulting in changes in phenotypes of ...
DOI:
10.1016/j.animal.2022.100496

20. Phenotypic plasticity in Populus trichocarpa clones across environments in the Nordic–Baltic region

Author:
Ann Christin Rönnberg-Wästljung; Anneli Adler; Almir Karacic; Kaspars Liepins; Thomas J. Richards; Pär K. Ingvarsson; Martin Weih
Source:
Scandinavian journal of forest research 2022 v.37 no.1 pp. 1-5
ISSN:
1651-1891
Subject:
phenotypic correlation,   etc   ; Populus trichocarpa; biocompatible materials; biofuels; forests; genotype-environment interaction; phenology; phenotypic plasticity; research; woody biomass; Latvia; Sweden;     Show all 12 Subjects
Abstract:
... Transition towards a bio-based society requires large amounts of woody biomass to be converted into biofuels and biomaterials. Populus species are good candidates for growth in short rotations, but there is a lack of climate-adapted plant material suitable for growth at the high latitudes of the Nordic–Baltic region. Here we studied the growth and phenology traits in 63 Populus trichocarpa clones ...
DOI:
10.1080/02827581.2022.2039279